Identification of Medically Actionable Secondary Findings in the 1000 Genomes

The American College of Medical Genetics and Genomics (ACMG) recommends that clinical sequencing laboratories return secondary findings in 56 genes associated with medically actionable conditions. Our goal was to apply a systematic, stringent approach consistent with clinical standards to estimate the prevalence of pathogenic variants associated with such conditions using a diverse sequencing reference sample. Candidate variants in the 56 ACMG genes were selected from Phase 1 of the 1000 Genomes dataset, which contains sequencing information on 1,092 unrelated individuals from across the world. These variants were filtered using the Human Gene Mutation Database (HGMD) Professional version and defined parameters, appraised through literature review, and examined by a clinical laboratory specialist and expert physician. Over 70,000 genetic variants were extracted from the 56 genes, and filtering identified 237 variants annotated as disease causing by HGMD Professional. Literature review and expert evaluation determined that 7 of these variants were pathogenic or likely pathogenic. Furthermore, 5 additional truncating variants not listed as disease causing in HGMD Professional were identified as likely pathogenic. These 12 secondary findings are associated with diseases that could inform medical follow-up, including cancer predisposition syndromes, cardiac conditions, and familial hypercholesterolemia. The majority of the identified medically actionable findings were in individuals from the European (5/379) and Americas (4/181) ancestry groups, with fewer findings in Asian (2/286) and African (1/246) ancestry groups. Our results suggest that medically relevant secondary findings can be identified in approximately 1% (12/1092) of individuals in a diverse reference sample. As clinical sequencing laboratories continue to implement the ACMG recommendations, our results highlight that at least a small number of potentially important secondary findings can be selected for return. Our results also confirm that understudied populations will not reap proportionate benefits of genomic medicine, highlighting the need for continued research efforts on genetic diseases in these populations.     

Children and marital satisfaction in a non-Western sample: having more children increases marital satisfaction among the Igbo people of Nigeria

Previous research has demonstrated that having more children decreases marital satisfaction among parents. However, the universality of these findings is limited since the vast majority of the studies have been conducted in Western countries. In the present study, 374 people from the Igbo ethnic group (Nigeria) were assessed for levels of marital satisfaction and the number of children. In contrast to almost all previous findings, we found a positive relationship between the number of children and marital satisfaction among parents. Number of children was the strongest predictor of marital satisfaction even when compared to other variables like wealth and education. Our results suggest that the negative relationship between the number of children and marital satisfaction is not culturally universal and probably only characterizes developed, individualistic Western countries. We discuss our findings from a sociocultural and evolutionary perspective.     

Two novel loci underlie natural differences in Caenorhabditis elegans abamectin responses

Parasitic nematodes cause a massive worldwide burden on human health along with a loss of livestock and agriculture productivity. Anthelmintics have been widely successful in treating parasitic nematodes. However, resistance is increasing, and little is known about the molecular and genetic causes of resistance for most of these drugs. The free-living roundworm Caenorhabditis elegans provides a tractable model to identify genes that underlie resistance. Unlike parasitic nematodes, C. elegans is easy to maintain in the laboratory, has a complete and well annotated genome, and has many genetic tools. Using a combination of wild isolates and a panel of recombinant inbred lines constructed from crosses of two genetically and phenotypically divergent strains, we identified three genomic regions on chromosome V that underlie natural differences in response to the macrocyclic lactone (ML) abamectin. One locus was identified previously and encodes an alpha subunit of a glutamate-gated chloride channel (glc-1). Here, we validate and narrow two novel loci using near-isogenic lines. Additionally, we generate a list of prioritized candidate genes identified in C. elegans and in the parasite Haemonchus contortus by comparison of ML resistance loci. These genes could represent previously unidentified resistance genes shared across nematode species and should be evaluated in the future. Our work highlights the advantages of using C. elegans as a model to better understand ML resistance in parasitic nematodes.     

Where ichthyofaunal provinces meet: the fish fauna of the Lake Edward system,East Africa

Based on literature, museum collections and three recent expeditions, an annotated species list of the Lake Edward, East Africa, drainage system is presented, excluding the endemic haplochromines. A total of 34 non-Haplochromis species belonging to 10 families and 21 genera are recorded from the system. Three of these are endemic and two others have been introduced in the region. Six species are new records for the Lake Edward system. A species accumulation curve indicates that we probably covered most of the non-Haplochromis species in the area sampled during the recent expeditions, but undetected species might still be present in the Congolese part of the system, which is poorly sampled. A comparison of the species list with those of neighbouring basins confirmed the placement of the Lake Edward system within the east-coast ichthyofaunal province.